PACTS-Assisted Thermal Proteome Profiling for Use in Identifying Peptide-Interacting Proteins
Bioactive peptides play important roles in various biological processes. However, the traditional methods for profiling the peptide-interacting proteins require modifications to the peptide molecules, often leading to false identifications. We found that the interaction between peptide ligands and p...
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Veröffentlicht in: | Analytical chemistry (Washington) 2022-05, Vol.94 (18), p.6809-6818 |
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creator | Zhao, Ting Tian, Jingya Wang, Xiankun Hao, Yanan Xu, Mengting Zhao, Yuanyuan Liu, Xinyue Chen, Yali Jia, Chenxi |
description | Bioactive peptides play important roles in various biological processes. However, the traditional methods for profiling the peptide-interacting proteins require modifications to the peptide molecules, often leading to false identifications. We found that the interaction between peptide ligands and protein receptors induced significant changes in the abundance of the interacting proteins, which is a signature indicating the interaction and providing complementary information for use in the classical thermal proteome profiling (TPP) technique. Herein, we developed a novel Peptide-ligand-induced Abundance Change of proTeinS (PACTS)-assisted TPP strategy for the identification of peptide-interacting proteins based on the peptide-ligand-induced change in protein abundance. The utility and efficacy of this approach were demonstrated by the identification of the interaction of the protein 3-phosphoinositide-dependent protein kinase 1 (PDPK1) and PDPK1-interacting fragment (PIF) pair and by large-scale profiling of the interacting proteins of PIF. The PACTS-assisted TPP approach was applied to describe the interactome of amyloid beta (Aβ) 1-42 in THP-1 cells and resulted in the identification of 103 interacting proteins. Validation experiments indicated that Aβ1-42 interacted directly with fatty acid synthase and inhibited its enzymatic activity, providing insights into fatty acid metabolic disorders in Alzheimer’s disease (AD). Overall, PACTS-assisted TPP is an efficient approach, and the newly identified Aβ-interacting proteins provide rich resources for the research on AD. |
doi_str_mv | 10.1021/acs.analchem.2c00581 |
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However, the traditional methods for profiling the peptide-interacting proteins require modifications to the peptide molecules, often leading to false identifications. We found that the interaction between peptide ligands and protein receptors induced significant changes in the abundance of the interacting proteins, which is a signature indicating the interaction and providing complementary information for use in the classical thermal proteome profiling (TPP) technique. Herein, we developed a novel Peptide-ligand-induced Abundance Change of proTeinS (PACTS)-assisted TPP strategy for the identification of peptide-interacting proteins based on the peptide-ligand-induced change in protein abundance. The utility and efficacy of this approach were demonstrated by the identification of the interaction of the protein 3-phosphoinositide-dependent protein kinase 1 (PDPK1) and PDPK1-interacting fragment (PIF) pair and by large-scale profiling of the interacting proteins of PIF. The PACTS-assisted TPP approach was applied to describe the interactome of amyloid beta (Aβ) 1-42 in THP-1 cells and resulted in the identification of 103 interacting proteins. Validation experiments indicated that Aβ1-42 interacted directly with fatty acid synthase and inhibited its enzymatic activity, providing insights into fatty acid metabolic disorders in Alzheimer’s disease (AD). Overall, PACTS-assisted TPP is an efficient approach, and the newly identified Aβ-interacting proteins provide rich resources for the research on AD.</description><identifier>ISSN: 0003-2700</identifier><identifier>EISSN: 1520-6882</identifier><identifier>DOI: 10.1021/acs.analchem.2c00581</identifier><identifier>PMID: 35485935</identifier><language>eng</language><publisher>United States: American Chemical Society</publisher><subject>3-Phosphoinositide-Dependent Protein Kinases ; Alzheimer Disease - metabolism ; Alzheimer's disease ; Amyloid beta-Peptides - chemistry ; Analytical chemistry ; Biological activity ; Chemistry ; Enzymatic activity ; Fatty acids ; Fatty-acid synthase ; Humans ; Kinases ; Ligands ; Metabolic disorders ; Neurodegenerative diseases ; Peptide Fragments - metabolism ; Peptides ; Protein kinase ; Proteins ; Proteome - metabolism ; Proteomes</subject><ispartof>Analytical chemistry (Washington), 2022-05, Vol.94 (18), p.6809-6818</ispartof><rights>2022 American Chemical Society</rights><rights>Copyright American Chemical Society May 10, 2022</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a376t-2bb848540613daccfa7ed0bca5d846ef4fea55e4cdb492d6fdf337cea5b62ef43</citedby><cites>FETCH-LOGICAL-a376t-2bb848540613daccfa7ed0bca5d846ef4fea55e4cdb492d6fdf337cea5b62ef43</cites><orcidid>0000-0001-6334-5282</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/acs.analchem.2c00581$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/acs.analchem.2c00581$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,780,784,2765,27076,27924,27925,56738,56788</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35485935$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhao, Ting</creatorcontrib><creatorcontrib>Tian, Jingya</creatorcontrib><creatorcontrib>Wang, Xiankun</creatorcontrib><creatorcontrib>Hao, Yanan</creatorcontrib><creatorcontrib>Xu, Mengting</creatorcontrib><creatorcontrib>Zhao, Yuanyuan</creatorcontrib><creatorcontrib>Liu, Xinyue</creatorcontrib><creatorcontrib>Chen, Yali</creatorcontrib><creatorcontrib>Jia, Chenxi</creatorcontrib><title>PACTS-Assisted Thermal Proteome Profiling for Use in Identifying Peptide-Interacting Proteins</title><title>Analytical chemistry (Washington)</title><addtitle>Anal. Chem</addtitle><description>Bioactive peptides play important roles in various biological processes. However, the traditional methods for profiling the peptide-interacting proteins require modifications to the peptide molecules, often leading to false identifications. We found that the interaction between peptide ligands and protein receptors induced significant changes in the abundance of the interacting proteins, which is a signature indicating the interaction and providing complementary information for use in the classical thermal proteome profiling (TPP) technique. Herein, we developed a novel Peptide-ligand-induced Abundance Change of proTeinS (PACTS)-assisted TPP strategy for the identification of peptide-interacting proteins based on the peptide-ligand-induced change in protein abundance. The utility and efficacy of this approach were demonstrated by the identification of the interaction of the protein 3-phosphoinositide-dependent protein kinase 1 (PDPK1) and PDPK1-interacting fragment (PIF) pair and by large-scale profiling of the interacting proteins of PIF. The PACTS-assisted TPP approach was applied to describe the interactome of amyloid beta (Aβ) 1-42 in THP-1 cells and resulted in the identification of 103 interacting proteins. Validation experiments indicated that Aβ1-42 interacted directly with fatty acid synthase and inhibited its enzymatic activity, providing insights into fatty acid metabolic disorders in Alzheimer’s disease (AD). 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Chem</addtitle><date>2022-05-10</date><risdate>2022</risdate><volume>94</volume><issue>18</issue><spage>6809</spage><epage>6818</epage><pages>6809-6818</pages><issn>0003-2700</issn><eissn>1520-6882</eissn><abstract>Bioactive peptides play important roles in various biological processes. However, the traditional methods for profiling the peptide-interacting proteins require modifications to the peptide molecules, often leading to false identifications. We found that the interaction between peptide ligands and protein receptors induced significant changes in the abundance of the interacting proteins, which is a signature indicating the interaction and providing complementary information for use in the classical thermal proteome profiling (TPP) technique. Herein, we developed a novel Peptide-ligand-induced Abundance Change of proTeinS (PACTS)-assisted TPP strategy for the identification of peptide-interacting proteins based on the peptide-ligand-induced change in protein abundance. The utility and efficacy of this approach were demonstrated by the identification of the interaction of the protein 3-phosphoinositide-dependent protein kinase 1 (PDPK1) and PDPK1-interacting fragment (PIF) pair and by large-scale profiling of the interacting proteins of PIF. The PACTS-assisted TPP approach was applied to describe the interactome of amyloid beta (Aβ) 1-42 in THP-1 cells and resulted in the identification of 103 interacting proteins. Validation experiments indicated that Aβ1-42 interacted directly with fatty acid synthase and inhibited its enzymatic activity, providing insights into fatty acid metabolic disorders in Alzheimer’s disease (AD). Overall, PACTS-assisted TPP is an efficient approach, and the newly identified Aβ-interacting proteins provide rich resources for the research on AD.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>35485935</pmid><doi>10.1021/acs.analchem.2c00581</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0001-6334-5282</orcidid></addata></record> |
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subjects | 3-Phosphoinositide-Dependent Protein Kinases Alzheimer Disease - metabolism Alzheimer's disease Amyloid beta-Peptides - chemistry Analytical chemistry Biological activity Chemistry Enzymatic activity Fatty acids Fatty-acid synthase Humans Kinases Ligands Metabolic disorders Neurodegenerative diseases Peptide Fragments - metabolism Peptides Protein kinase Proteins Proteome - metabolism Proteomes |
title | PACTS-Assisted Thermal Proteome Profiling for Use in Identifying Peptide-Interacting Proteins |
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